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Supplementary Figures and Legends

Supplementary Table ST2: a) Arabidopsis thaliana genotypes and seed stocks used. b) Number of high quality

samples for the frequency-normalized table (top) and the rarefaction normalized table (bottom), in which some

replicate samples were pooled to make the rarefaction threshold. Does not include the four sterile seedling samples

(Supplementary Figure S13).

Supplementary Table ST4: Percent variance explained by each variable in the Full GLMM.

Supplementary Table ST5: ANOVA statistics comparing Shannon Diversity and taxonomic distributions across the S,

R, and EC fractions. This table accompanies Figure 2, Supplementary Figure S7, and Supplementary Figure S15. It is

provided as a separate Excel document with statistics on rarefaction-normalized data on Sheet 1, and statistics on

frequency-normalized data on Sheet 2. Further explanation is given in the table.

(as separate Excel document available from Nature website)

Supplementary Table ST3: All 778 Measurable OTUs including GLMM predictions, taxonomic assignments,

sequences, and location of notable OTUs within main figures. Provided as a separate Excel document with a full table

legend on Sheet 1, the table based on rarefaction -normalized data on Sheet 2, and the table based on frequency-

normalized data on Sheet 3.

(as separate Excel document available from Nature website)

Supplementary Figure S1: Harvesting scheme. a) Using gloves and a flame-sterilized work surface, plants are

overturned, pots are removed, and soil is crumbled/brushed away leaving ≤1 mm rhizosphere soil on roots. b) The

above-ground parts are cut away and rhizosphere soil is harvested from roots by shaking them in sterile phosphate

buffer with Silwet L-77; the rinse is pelleted and becomes the rhizosphere R fraction. c) Roots are placed in a new

tube with sterile phosphate buffer and sonicated for five 30 second bursts at low intensity (see Supplementary

Methods). The surface-cleaned roots are then snap frozen and lyophilized to become the EC fraction. d) SEM

showing intact root surface after rhizosphere soil has been removed, but prior to sonication. Scale = 100 microns. e)

SEM showing a root-surface bacterium on root shown in d. Scale = 1 micron. f) SEM showing the disruptive clearing

of nearly the entire root surface after sonication. Scale = 100 microns.

Supplementary Figure S2: Primer test and technical reproducibility. a) Position on the 16S gene of each of the primers

tested. b) Sequence of each primer used. c) Composition of the 13 samples tested. d) Log10 transformation of raw reads per

OTU for one independent replicate (x-axis) vs. the other (y-axis), where both replicates were PCR-amplified and sequenced

from the same sample (axes labels are transformed and cover a range of 0-10,000 reads). The intersection of the red lines

shows where an OTU with 25 reads in both replicates would lie. e) Progressive drop-out analysis displaying the R2 correlation

of the data in d as OTUs with low read numbers are discarded. When only OTUs with ≥25 reads are considered (red line) the

R2 is acceptable at 0.87, a balance between reproducibility and data loss for low-abundance OTUs. In f-i, green circles are

EC samples, blue triangles are R samples, and black squares are bulk soil samples. f) Total reads obtained from amplicons

made with 804F, 926F, or 1114F paired with bar-coded 1392R. g) Percent of the ‘usable’ reads from f which are not identified

as plant or chimeric OTUs. h) Shannon-Weiner species diversity of 1000 usable reads (for each sample with ≥1000 reads). i)

Chao1 diversity of 1000 usable reads from each sample (for each sample with ≥1000).

Supplementary Figure S3: Informatics pipeline. Order of events. Broken-line black-line boxes represent files. Blue

double-line boxes describe events that occur locally using custom scripts. Red boxes describe events that are implemented

through QIIME/OTUpipe.

Supplementary Figure S4: Sequencing statistics and quality. a) Sequencing depth per sample in reads for the

three sample fractions S, R, and EC. Each dot represents a single plant or soil sample. Within each fraction, the total

(t), usable (u), and measurable (m) read counts are shown for all samples. The box plots contain the 1st and 3rd

quartiles, split by the median; whiskers extend to include the farthest outliers. b) Rarefaction curves to 10,000

sequences for cumulative reads from S, R, and EC fractions considering all usable OTUs (top) and only measurable

OTUs (bottom) c) Table, split by sample fraction, summarizing: cumulative numbers of total high quality reads,

‘usable’ (non-plant & non-chimera) reads, number of OTUs after the technical reproducibility ‘25x5’ threshold is

applied, ‘measurable’ reads (reads contained in OTUs that pass the 25x5 threshold). d) Shannon diversity of

individual samples from each fraction, calculated from the rarefaction-normalized table, before (left) and after (right)

applying the 25x5 measurable OTU threshold.

Supplementary Figure S5: Sample fraction and soil type drive the microbial composition of root-associated

endophyte communities. a) Principal Coordinate Analysis (PCoA) of pairwise normalized weighted Unifrac distances

between the samples considering relative abundance of all (unthresholded) OTUs. b) The median RAs for the 25x5

thresholded ‘measurable’ OTUs from each of 24 soil/stage/fraction groups were log2 transformed (see methods) to make 24

representative samples (branch labels) and the pairwise Bray Curtis Similarity was used to hierarchically cluster these

representatives (group average linkage).

Supplementary Figure S6: OTUs identified from four independent biological replicates are reproducible. Heat map

displaying the reproducibility between four independent replicates at the yng developmental stage of bulk soil (squares),

Col-0 R samples (triangles), and Col-0 EC samples (circles). Each symbol represents the median of six or more samples.

All data were log2 transformed for visualization, but for ease of interpretation the quantities shown in the color key represent

the original (untransformed) counts (in panel a) and frequencies (in panel b) for each color. Although all 778 measurable

OTUs were included, some OTUs had a median of 0 in all Col-0 and soil groups shown and were removed from the display.

0 102 1 10

0 10 0.1 1

0 13 0.1 1

Figure S7: OTUs that differentiate the endophyte compartment and rhizosphere from soil. A, Heat map displaying the

median RA (log2 transformed) of each of 108 ‘R and EC-differentiating OTUs’ present across experimental replicates, where

samples and OTUs are clustered on their Bray Curtis Similarity (group average linkage). The color key relates the colors to the

untransformed RAs. B, The strength of the GLMM predictions (Best Linear Unbiased Predictors or BLUPs) is represented by the

height of the bars. a, shows OTUs predicted as EC–enriched (red, up) or EC depleted (blue, down). b, shows OTUs found higher

in the EC in MF soil than CL (brown, up) or higher in CL than MF (gold, down). OTUs in a that are not differentially affected by

soil type as are shown in darker hues in a. c, OTUs predicted as R-enriched (as in a above). d OTUs higher in R in one soil type

(as in b). C) Histogram displaying the distribution of the phyla present in the 778 measurable OTUs in soil (S), rhizosphere (R)

and endophytic compartments (EC) compared to phyla present in the subset of EC OTUs enriched (EC-Up), or depleted (EC-

Down) compared to soil. Shannon Diversity (considering phyla as individuals) is shown above. A differential number of asterisks

above the Shannon Diversity values represents a significant difference (p<0.05, weighted ANOVA, Supplementary Methods,

Supplementary Table ST5) D) Distribution of families present among the OTUs of the phylum Actinobacteria. E) Distribution of

families present among the OTUs of the phylum Proteobacteria. F) Distribution of families present among the OTUs of three

classes of the phylum Proteobacteria – Alpha (left), Beta (center), Gamma (right). Statistical evidence for presence, enrichment

in, or depletion from EC is detailed in Supplementary Table S6. Data in (D-F) are from both soil types, pooled (see

Supplementary Figure S15 for each soil separately).

Supplementary Figure S8: Overlap of GLMM predictions between rarefaction-normalized and frequency-

normalized OTU tables. The number of OTUs predicted by the full GLMM in each category that are unique to the

frequency table is shown in orange. The number of OTUs predicted by the full GLMM in each category that are unique to

the rarefied table are shown in green. The number of OTUs that were shared predictions in the two tables is shown in

black.

Supplementary Figure S9: 16S taxonomy classification at the family level is robust to method. For taxonomy-

supervised classification, reads that passed default QIIME quality thresholds (but that were not clustered into OTUs) were

trimmed to 220bp and were classified via RDP against Greengenes (Feb. 4 2011 version) training set to get family-level

taxonomy. The abundance of each family was compared to the abundance of that family when the family assignments

were assigned after the taxonomy-unsupervised grouping of reads into OTUs. In a) The total reads from non-chloroplast

families from both taxonomy-supervised and taxonomy-unsupervised methods were rarefied to 10,000,000 reads, and the

reads per family are shown as the log2 transformed relative abundance of the total reads, whereas b) shows the relative

abundance of each family using all non-chloroplast reads, omitting the rarefaction step. The scatterplots thus show the

high correlation at the family level for supervised and unsupervised taxonomy assignment. The dataset used for this figure

included extra samples not described here, and was clustered as a single .fasta using the default QIIME implementation of

Uclust 28.

Supplementary Figure S10: Test for PCR bias in

pyrotagging. a) Relative abundance of 16S

metagenomics and pyrotag reads. To assess

possible bias introduced by amplification for

pyrotagging, we compared the taxonomic

distribution of a metagenome library created without

amplification with a corresponding pyrotag dataset.

Both datasets are from Col-0 Mason Farm young

samples. 16S rDNA reads from this metagenome

library (One HiSeq lane; more than 400 million 150

bp paired-end reads) were extracted by alignment

against the 16S Silva database (release 106).

Aligned reads were then assigned a taxonomy using

an RDP training set built with the Greengenes

reference database (version: May 9th 2011). This

allowed classification of 57,663 16S reads from the

metagenome sample using a bootstrap threshold

>=0.50. There is an excellent overall correlation

between the relative abundance of pyrotags and

metagenome 16S rDNA reads across the major

phyla represented in the datasets. Only two major

classes, Thaumarchaeota and Planctomycea, were

not amplified by the 1114F-1392R primers. Slightly

higher abundance of Actinobacteria and

Betaproteobacteria was observed in pyrotag data

than in metagenome 16S reads. This was

investigated further. b) For those classes in which

underrepresentation in the pyrotag data are

observed (red class names in Supplemental Figure

S10a), we used in silico PCR analyses using the

Greengenes database as template and our pyrotags

primer pair, allowing a maximum of 2 mismatches,

to investigate at which taxonomic level the under-

representation would be discerned (Supplemental

Figure S10b). We show that Thaumarchaeota

(class) and Planctomycea (class) may be

misrepresented in our pyrotag data. Since the

Greengenes database contains many sequences

amplified with the 1392R primer and therefore lacks

this primer’s sequence, we removed all sequences

shorter than 6449 (in absolute position) in our

reference database to minimize false negative rate

(i.e. sequences not amplifying because they are not

long enough to match the 1392R primer sequence).

Supplementary Figure 11: Dot plots of notable OTUs. Relative abundance for each OTU (number at top of each panel; keyed

to Supplementary Table ST3) from the frequency-normalized table was log2 transformed and the abundance for each sample (y-

axis) plotted as an individual symbol. The y-axis is labeled with the actual (untransformed) relative abundance values. In a-h,

each position on the x-axis is labeled with a symbol to represent the sample group (legend, lower right), and samples from that

group are plotted column-wise directly above. Biological replicates are shown in the same column with different hues. The

median of each biological replicate is shown with a horizontal black bar; some may not be visible because they are at 0. In i and

j, sample color is according to the legend, and each position on the x-axis is labeled by Arabidopsis accession, with samples

from that accession plotted above each label. Each OTU in the figure has model predictions in several categories (Supplemental

table ST3).

Supplementary Figure S12: Quantification of microbes in the three sample fractions using CARD-FISH. Four sets of

Col-0 roots were pooled, processed, diluted, and put onto filters. (a) CARD-FISH using the EUB338, eubacterial probe, was

applied and counterstained with DAPI. The number of EUB positive signals co-localizing with a DAPI signal was counted and

the number of EUB positive signals per sample was calculated. This is an estimate for the number of bacteria present in

each of our samples that DNA was extracted from with bulk soil (n=40), rhizosphere (n=39), and endophytic compartment

(n=40). * indicates statistical significance at p<1x1016 (ANOVA with post-hoc TukeyHSD) between each of the sample

groups (b) Using double CARD-FISH on filters made from equal concentration of the 3 sample fractions, we determined the

% of DAPI positive eubacteria that are also co-localize with either the HGC69a (Actinobacteria) or Brady4

(Bradyrhizobiaceae) probes on filters made from bulk soil (n=10), rhizosphere (n=10), and endophytic compartment (n=10)

samples. Actinobacteria was in higher abundance in EC samples and Bradyrhizobiaceae was in lower abundance in EC

samples compared to soil and R samples as expected from our pyrotag sequencing data. (c) Double CARD-FISH was

applied using the EUB338, eubacterial probe (green) and the Brady4, Bradyrhizobiaceae probe (red), counterstained with

DAPI (the asterisks indicate signals that are positive in all 3 channels). (d) Newly forming lateral roots and root tips were

found commonly to be heavily colonized. Scale bars represent 50 microns.

Supplementary Figure S13: Pyrosequencing of sterile seedlings as compared to vs. non-sterile EC samples. DNA was

extracted from homogenates from gnotobiotic seedlings of the genotypes Col-0, Cvi-0, Sha-0, and Tsu-0 (from which no

culturable microbes were found), using bacteriolytic DNA preps, and these were pyrosequenced and clustered into OTUs as

part of our full dataset. 21935, 20747, 23141, and 20272 high quality reads were obtained from each gnotobiotic genotype,

respectively (triangles). The same total number of total reads was sampled from using pooled EC data from the full dataset for

these accessions (circles). Each position on the X axis represents an OTU in the full dataset (measurable OTUs on top, rare

OTUs on bottom) and the position on the Y axis represents the number of sequence reads found in that OTU. Both axes are

shown in log scale. Of the 86095 HQ reads obtained from both sterile plants and non-sterile plants, the majority were from

chloroplast OTUs (not shown). Far more non-plant reads were obtained from the non-sterile plants (19093 of 86095, or 22%)

vs. sterile plants (34 of 86095, or 0.04%), a difference approaching three orders of magnitude. The 34 reads from non-sterile

plants were members of 31 OTUs (triangles – some overlap on the log-scale axis). No OTU in a sterile plant sample was

represented by more than one read, and only two OTUs were shared by more than one of the accessions - both of these

shared OTUs were not in the measurable set, and had poor taxonomic classification. 11 of these 31 OTUs were not

represented in the non-sterile samples. Furthermore, by including extra unused barcodes in our mapping files, or by sequencing

sterile water in excess, we have been able to occasionally 'detect' single representatives of OTUs in our dataset, demonstrating

that technical noise can cause singletons (data not shown). While we cannot rule out that unculturable microbes survive surface

sterilization and exist at extremely low abundance, we have no evidence that such microbes exist in A. thaliana roots.

Supplementary Figure S14: Genotype-variable OTUs colored by sequence plate. Displays the data from Fig. 3i (MF

old EC, left) and Fig. 3j (CL old EC right), colored by sequence plate (instead of biological replicate as in Figure 3)

according to the legend within each plot. The top panel is based on rarefied data, as in Figure 3, and the bottom panel is

based on the relative abundance, as in Supplementary Figure S11. (Note: ‘a’ and ‘b’ in our plate naming scheme do not

represent different regions of the same plate. All 454 regions were modeled independently in the Full GLMM).

Supplementary Figure S15: Phyla in each sample fraction by soil type. Histogram displaying the distribution of the

phyla present in the 778 measurable OTUs in soil (S), rhizosphere (R) and endophytic compartments (EC) with each soil

type, MF and CL, considered independently. Rarefaction-normalized on top; frequency-normalized on bottom.

Accompanying statistics on the distributions are in Supplementary Table ST5.